In 1978, it was reported for the first time that an antisense molecule inhibited infection with influenza virus. Then, reports that antisense molecules inhibited oncogene expression and AIDS infection were also made. Since antisense oligonucleotides specifically control the expression of undesirable genes, they are one of the fields that have been expected most as pharmaceuticals in recent years.
The antisense method is based on the concept that in a series of steps during flow according to the so-called central dogma, DNA→mRNA→protein, the process of translation from MRNA to protein is to be controlled with the use an antisense oligonucleotide complementary to mRNA.
However, when a native oligonucleotide is applied to this method as an antisense molecule, there have been problems that it is degraded by various in vivo nucleases, or its permeation through the cell membrane is not high. Therefore, the inventors of the present invention performed the synthesis of a nucleoside analogue unit which has the following general formula                 where Base represents a purine or pyrimidine nucleic acid base or its modification product,and in which the conformation of the sugar moiety has been fixed. They found that oligonucleotide derivatives prepared with the use of the nucleoside analogue unit are useful as antisense molecules, and they filed a patent application covering the oligonucleotide derivatives (Japanese Unexamined Patent Publication No. 1998-304889).        
On the other hand, a method which comprises targeting double-stranded gene DNA, and effecting direct binding to the double-stranded DNA to form a triplex, thereby suppressing transcription to mRNA is called the antigene method. With the antigene method, it is known that triplex-forming oligonucleotides (TFO's) used as antigene molecules bind to the homopurine tract in double-stranded DNA via Hoogsteen hydrogen bonding or reverse Hoogsteen hydrogen bonding. Generally, the former mode of bonding is widely used (P. P. Chan and P. M. Glazer, J. Mol. Med., 75, 267-282(1997)).
Chemical formulas illustrating typical examples of the modes of bonding for triplex-forming Hoogsteen bonding and reverse Hoogsteen bonding are shown below. where the two modes of bonding represented by a are T:A:T and C+:G:C bondings which are Hoogsteen bondings, while the two modes of bonding represented by b are A:T:A and G:G:C bondings which are reverse Hoogsteen bondings.
According to these modes of bonding, thymine is hydrogen-bonded to adenine of an AT base pair, and cytosine having the nitrogen atom at the 3-position protonated is hydrogen-bonded to guanine of a GC base pair. That is, the nitrogen atom at the 3-position of the cytosine base in an oligonucleotide has to be protonated in order to recognize a duplex containing a GC base pair and form a stable triplex. Thus, the triplex is stabilized under acidic conditions, but the triplex-forming ability is not sufficient in the in vivo pH range. Various other problems for the formation of a stable triplex remain to be solved, such that the targeted sequence is limited to the homopurine tract.
To solve these problems, numerous triplex-forming nucleoside analogues have been reported. Of them, the analogue methylated at the 5-position of cytosine (5-methylcytosine) is known to recognize a GC base pair specifically, enhancing a triplex-forming ability. Thus, this analogue has been widely used in conventional triplex-forming oligonucleotides (T. J. Povsic and P. B. Dervan, J. Am. Chem. Soc., 111, 3059-3061(1989)).
However, if a pyrimidine base is present in a homopurine tract, the target sequence of double-stranded DNA, the stability of the resulting triplex markedly. decreases, and this poses a serious problem in the antigene method. In this connection, T, a native nucleic acid base, has been reported to be capable of recognizing a CG base pair (Yoon, K. et al., (1992) Proc. Natl. Acad. Sci. USA, 89, 3840-3844). However, its ability is not satisfactory for practical use, and there has been a demand for the development of an oligonucleotide derivative which can specifically recognize a CG base pair present in a homopurine tract and has a high triplex-forming ability.